Contacts of the helix formed by residues 34 - 53 (chain C) in PDB entry 5NJ8
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 34 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C LYS 4.1 2.5 - - - +
33C SER* 1.3 76.2 - - - +
35C PRO* 1.3 76.3 - - + +
36C SER* 3.3 15.1 + - - -
37C LYS* 3.1 47.5 + - - +
38C ARG* 3.5 13.7 + - - +
40C ARG* 4.2 8.4 + - - +
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Residues in contact with PRO 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C ASN* 1.3 90.0 - - + +
36C SER* 1.3 61.8 + - - +
38C ARG* 3.5 34.8 + - - +
39C HIS* 3.4 17.3 + - - +
42C ARG* 4.8 1.7 + - - -
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Residues in contact with SER 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C ASN* 3.2 13.1 - - - +
35C PRO* 1.3 80.3 - - - +
37C LYS* 1.3 68.2 + - - +
39C HIS* 2.9 11.1 + - - +
40C ARG* 2.8 37.9 + - - +
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Residues in contact with LYS 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C LYS 2.8 27.3 + - - +
33C SER* 3.5 18.4 - - - +
34C ASN* 3.1 31.6 + - - +
36C SER* 1.3 78.3 - - - +
38C ARG* 1.3 57.5 + - + +
40C ARG* 3.7 25.5 - - - +
41C ASP* 2.8 56.7 + - - +
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Residues in contact with ARG 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C SER* 4.0 25.2 + - - +
34C ASN 3.5 6.3 + - - +
35C PRO* 3.5 49.0 + - - +
36C SER 3.2 0.6 - - - -
37C LYS* 1.3 78.6 - - + +
39C HIS* 1.3 57.9 + - - +
41C ASP* 3.8 5.3 - - - +
42C ARG* 3.0 61.5 + - - +
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Residues in contact with HIS 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C PRO 3.4 9.8 + - - +
36C SER* 2.9 14.2 + - - +
38C ARG* 1.3 76.2 - - - +
40C ARG* 1.3 71.3 + - - +
42C ARG* 3.1 26.4 + - + +
43C LEU* 2.9 48.9 + - + +
128D LYS* 5.6 7.8 - - + +
129D LEU* 5.1 12.6 + - + +
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Residues in contact with ARG 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C ASN* 4.2 8.9 + - - +
36C SER* 2.8 30.6 + - - +
37C LYS* 3.7 43.5 - - - +
39C HIS* 1.3 76.0 - - + +
41C ASP* 1.3 63.5 + - - +
43C LEU* 3.0 9.7 + - - +
44C ASN* 2.8 41.7 + - - +
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Residues in contact with ASP 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C LYS* 2.8 49.6 + - - +
38C ARG* 3.8 5.4 - - - +
40C ARG* 1.3 79.7 + - - +
42C ARG* 1.3 58.8 + - + +
44C ASN* 3.8 6.5 + - - +
45C THR* 2.5 37.3 + - - +
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Residues in contact with ARG 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C PRO 4.8 1.8 + - - -
38C ARG* 3.0 54.3 + - - +
39C HIS* 3.1 34.9 + - + +
41C ASP* 1.3 75.0 - - + +
43C LEU* 1.3 64.1 + - - +
45C THR* 3.1 7.2 + - - -
46C GLU* 3.0 25.5 + - - +
129D LEU* 4.5 24.0 - - + +
133D ARG* 4.3 18.6 - - - +
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Residues in contact with LEU 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C HIS* 2.9 33.8 + - + +
40C ARG* 3.4 9.6 - - - +
42C ARG* 1.3 75.8 - - - +
44C ASN* 1.3 70.5 + - - +
45C THR 2.9 1.0 + - - -
46C GLU* 2.9 4.7 + - - +
47C LEU* 2.8 29.3 + - + +
105D MET* 5.9 7.0 - - - -
109D ILE* 5.7 0.7 - - + -
128D LYS* 4.4 21.1 - - + -
129D LEU* 3.8 43.1 - - + +
132D LEU* 4.1 19.8 - - + +
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Residues in contact with ASN 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C ARG* 2.8 30.9 + - - +
41C ASP* 4.1 6.0 + - - +
43C LEU* 1.3 75.4 - - - +
45C THR* 1.3 56.6 + - - +
47C LEU* 4.0 8.8 - - - +
48C ASP* 2.9 29.6 + - - +
66C LYS* 3.6 34.4 + - - +
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Residues in contact with THR 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A ASP* 5.5 7.2 - - + -
41C ASP* 2.5 26.2 + - - +
42C ARG* 3.5 6.5 - - - -
44C ASN* 1.3 75.6 - - - +
46C GLU* 1.3 65.1 + - - +
48C ASP* 3.4 4.4 + - - +
49C ARG* 2.9 44.5 + - - +
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Residues in contact with GLU 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C ARG 3.0 10.9 + - - +
43C LEU 2.9 7.4 + - - +
45C THR* 1.3 81.8 - - - +
47C LEU* 1.3 57.2 + - - +
49C ARG* 3.6 6.7 + - - +
50C LEU* 2.9 26.5 + - - +
129D LEU* 4.7 6.9 - - + +
132D LEU* 4.2 12.1 - - + +
133D ARG* 3.6 55.8 + - + +
136D VAL* 3.6 22.3 - - + +
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Residues in contact with LEU 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C LEU* 2.8 18.3 + - + +
44C ASN* 4.0 8.5 - - - +
46C GLU* 1.3 75.6 - - - +
48C ASP* 1.3 62.5 + - - +
50C LEU* 3.2 7.3 + - + +
51C ALA* 2.9 24.8 + - + +
66C LYS* 3.7 41.3 - - + -
69C VAL* 3.7 29.1 - - + +
70C LEU* 4.3 30.5 - - + -
105D MET* 4.9 7.6 - - - -
132D LEU* 4.6 17.2 - - + +
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Residues in contact with ASP 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A LEU 5.1 5.5 - - - +
228A LEU 5.4 0.2 - - - -
229A ASP* 4.5 25.6 + - + +
44C ASN 2.9 20.3 + - - +
45C THR* 3.8 6.1 - - - +
47C LEU* 1.3 78.4 - - - +
49C ARG* 1.3 59.2 + - - +
51C ALA* 3.2 9.0 + - - +
52C SER* 2.9 30.8 + - - -
66C LYS* 6.0 2.0 - - - +
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Residues in contact with ARG 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A ASP* 4.4 21.4 - - - +
45C THR* 2.9 30.9 + - - +
46C GLU* 3.6 12.5 + - - +
48C ASP* 1.3 76.8 - - - +
50C LEU* 1.3 62.7 + - - +
52C SER* 2.9 27.1 + - - -
53C LEU* 3.2 25.4 - - + +
136D VAL* 4.1 20.6 - - + -
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Residues in contact with LEU 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C GLU 2.9 18.2 + - - +
47C LEU* 3.2 6.9 + - - +
49C ARG* 1.3 75.0 - - - +
51C ALA* 1.3 64.1 + - - +
53C LEU* 3.5 13.1 + - + +
54C LEU* 4.0 7.1 + - - +
69C VAL* 4.7 4.9 - - + -
70C LEU* 4.1 11.7 - - + -
73C SER* 3.9 22.0 - - - +
77C LEU* 6.3 0.4 - - + -
112D LEU* 4.8 7.0 - - + -
132D LEU* 3.5 28.5 - - + -
135D ALA* 4.6 6.3 - - + -
136D VAL* 3.8 30.7 - - + +
139D MET* 3.5 35.5 - - + +
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Residues in contact with ALA 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C LEU 2.9 8.9 + - - +
48C ASP* 3.4 15.3 - - - +
49C ARG 3.1 0.2 - - - -
50C LEU* 1.3 71.9 - - - +
52C SER* 1.3 52.5 + - - +
53C LEU 2.6 4.6 + - - -
54C LEU* 2.5 44.8 + - + +
61C ILE* 3.3 15.3 - - + +
69C VAL* 3.5 37.6 - - + +
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Residues in contact with SER 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C ASP* 2.9 16.4 + - - -
49C ARG* 2.9 29.5 + - - -
51C ALA* 1.3 73.5 - - - +
53C LEU* 1.3 66.6 + - - +
54C LEU 3.3 3.2 + - - +
61C ILE* 3.9 16.7 - - - +
143D ARG* 5.0 0.9 + - - -
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Residues in contact with LEU 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C ARG* 3.2 27.3 + - + +
50C LEU* 3.7 13.2 - - - +
51C ALA 2.6 5.6 + - - -
52C SER* 1.3 84.6 - - - +
54C LEU* 1.3 59.5 + - - -
136D VAL* 4.2 18.6 - - + +
139D MET* 3.5 17.1 - - + +
140D LYS* 3.9 37.0 - - + +
143D ARG* 2.8 36.6 + - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il